Dear Gromacs users!
I want to perform Covariance analysis of my x-ray data sets via g_covar -f trr.pdb -s x_ray.tpr -n index -o PCA_eigenval.xvg -v PCA_eigenvec.trr where trr.pdb is the trajectory made from the 30 x-ray structures (only c-alpha atoms were selected. How I could obtain x_ray.tpr file for such analysis? I've tried to use tpr from full atomic model of the same protein which I';ve simulated recently. For that p[rotein tpr file have been already created. From that model via make_ndx I've defined only backbone atoms corresponded to the atoms in my pdb ensemble. On the next step I've used tpbconv on protein.tpr with index file to make reduced tpr file with atoms corresponded to the backbone of the pdb-ensemble. Now when I run g_covar with my ensemble and reduced tpr file I obtain error *** glibc detected *** g_covar: malloc(): memory corruption: 0x00007f27df53e018 *** On other hand if I specify for g_covar full-atomic tpr file with the index ( where atoms corresponded to the trr.pdb are mentioned) g_covar -f trr.pdb -s protein.tpr -n index -o PCA_eigenval.xvg -v PCA_eigenvec.trr I obtain another error Calculating the average structure ... Reading frame 0 time 1.000 WARNING: number of atoms in tpx (575) and trajectory (575) do not match ------------------------------------------------------- Program g_covar, VERSION 4.5.5 Source code file: /tmp/build/gromacs-4.5.5/src/gmxlib/mshift.c, line: 102 Fatal error: Molecule in topology has atom numbers below and above natoms (575). You are probably trying to use a trajectory which does not match the first 575 atoms of the run input file. What I've done wrong and how I can define tpr file for trajectory made from several pdb files ? Thanks for help James -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists